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The International League Marlins were a transplanted version of the original Syracuse Chiefs. They were created on December 20, 1955, when the Syracuse club (a member of the IL as early as 1886 and a continuous member since 1934) was sold to Sidney Salomon (future founding owner of the St. Louis Blues of the National Hockey League) and Elliot Stein.

The 1955 Chiefs, an affiliate of the Philadelphia Phillies, finished only two games out of the playoffs, but drew only 85,000 fans, last in the eight-team league. In the Marlins' debut season in Miami, the club finished third and attracted 288,000 spectators, second in the IL circuit. Attendance dwindled in the years that followed, however, and by 1960 the Marlins—by then a Baltimore Orioles affiliate—were at the bottom of the IL, with fewer than 110,000 paying fans. The franchise signed a working agreement with the St. Louis Cardinals and moved to San Juan, Puerto Rico, in 1961, but after little more than a month of play the Marlins moved again to Charleston, West Virginia on May 19.

There was a separate franchise, also called the Miami Marlins, who played in the Florida State League from 1962–1970 and then from 1982–1988. They became the Miami Orioles from 1971–1981, and the Miami Miracle in 1989. Since 1992, they have been known as the Fort Myers Miracle.

In February 2008, it was announced that the big league Florida Marlins franchise would change its name to the Miami Marlins in 2012, upon moving into its new stadium at the former site of the Orange Bowl.

In June, 2013, a book titled: "THE FORGOTTEN MARLINS: A Tribute to the 1956-1960 Original Miami Marlins" was published by author Sam Zygner.

On July 20, 2013, the present-day Miami Marlins wore "throwback jerseys"/replicas of the International League Marlins' jerseys in a game against the Milwaukee Brewers at Miller Park.